Campaigners fear increases in peak fares could force commuters off trains while unions warn local stations may close if the government endorses plans to cut costs by changing the way the industry is run.

The transport secretary, Justine Greening, will set the direction of travel for the railways on Thursday with her official response to the McNulty review of the industry. She will also announce a new look at rail fares and a consultation on devolving powers over the network to local authorities.

The report by Sir Roy McNulty last year concluded that rail operating costs in Britain were 20%-30% higher than they should be and identified automatic ticketing and cutting staff on trains as potential savings. The government is expected broadly to endorse the proposals, which include sacrificing some ticket offices. Unions believe this could lead to station closures, job losses and higher fares.

Manuel Cortes, general secretary of the TSSA union, said: "If the local booking office goes, then the station will not be far behind. This will amount to a mini-Beeching with hundreds of stations in rural areas facing the threat of long-termclosure."

The Campaign for Better Transport has sounded alarm over fares, given McNulty's recommendation that the system should better manage peak demand by charging more for the busiest trains. Passengers already face fare rises 3% above inflation next year. Chief executive Stephen Joseph warned that many commuters have inflexible work times or commitments like childcare or school runs. Research suggested higher fares would have only a marginal impact on when people travelled.

He said: "If people could change their commute times easily, they would have done so by now to avoid having to stand on crowded trains. Raising the prices will simply create political opposition, price people on lower incomes off trains and make little difference to overcrowding."

Shadow transport secretary Maria Eagle said: "Plans to give train companies even greater freedoms to hike rail fares, close ticket offices and provide fewer staff on trains and at stations show just how out of touch ministers are with passengers and commuters.

Labour also warned against the government hastening the "deep alliances" that Network Rail has announced with train operators in the wake of McNulty in an attempt to work more closely together and drive down costs. Network Rail says the alliances, where train and track management will share regional offices, will "better align incentives and see quicker, more joined-up, decision making".

However, the RMT union says the plans mean "mini-Railtracks" and critics believe operators will in effect take control. Eagle said: "The same private companies who are already raking in large profits in an industry that receives £4bn of taxpayers' money every year are for the first time set to be given the whip hand over infrastructure as well as services."

The third strand of the government's rail reform package will be a consultation on devolving power over local railways to regional transport bodies — potentially opening up more of the country to the kind of integrated ticketing and services delivered in the capital by Transport for London now.

There was better news for part-time workers or parents working flexible hours. The government is indicating that it wants to see part-time commuter season tickets, offering discounts for regular passengers on the same journey who may not keep daily hours. In addition, Oyster-style smart ticketing is likely to be demanded from operators on future franchises. Rail minister Theresa Villiers said the technology offered the "potential for more flexible season tickets better suited to modern working practices".